Also another thing I noticed was that using

nf-core lint --fix

to update the

meta.yml

would create an updated topic block for the versions, where some attributes were of type

eval

, which also threw an error when linting. I had to swap those to

string

in my PR to get linting to chill (I just followed what the last merged module on main had done). Though I think this might have been brought up before.

in the same PR?

yes

it should be type eval...

Thanks Matthias. I’ll have another look. I’m pretty sure than when I added them as

eval

the linter was unhappy with me, but I don’t think I ever committed those changes to remote. I’ll try again and get back to you

be sure to have the latest dev version of tools for modules linting

i.e. the dev branch, not the latest release?

exactly

ok, tried again. the issue was the pre-commit, which does not like the committing of evals. Here’s the updated meta.yml:

name: "multivcfanalyzer"
description: SNP table generator from GATK UnifiedGenotyper with functionality
  geared for aDNA
keywords:
  - vcf
  - ancient DNA
  - aDNA
  - SNP
  - GATK UnifiedGenotyper
  - SNP table
tools:
  - "multivcfanalyzer":
      description: "MultiVCFAnalyzer is a VCF file post-processing tool tailored for
        aDNA. License on Github repository."
      homepage: "<https://github.com/alexherbig/MultiVCFAnalyzer>"
      documentation: "<https://github.com/alexherbig/MultiVCFAnalyzer>"
      tool_dev_url: "<https://github.com/alexherbig/MultiVCFAnalyzer>"
      doi: "10.1038/nature13591"
      licence:
        - "GPL >=3"
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - vcfs:
        type: file
        description: One or a list of uncompressed VCF file
        pattern: "*.vcf"
        ontologies: []
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - fasta:
        type: file
        description: Reference genome VCF was generated against
        pattern: "*.{fasta,fna,fa}"
        ontologies: []
  - - meta3:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - snpeff_results:
        type: file
        description: Results from snpEff in txt format (Optional)
        pattern: "*.txt"
        ontologies: []
  - - meta4:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - gff:
        type: file
        description: GFF file corresponding to reference genome fasta (Optional)
        pattern: "*.gff"
        ontologies: []
  - allele_freqs:
      type: boolean
      description: |
        Whether to include the percentage of reads a given allele is
        present in in the SNP table.
  - genotype_quality:
      type: integer
      description: |
        Minimum GATK genotyping threshold threshold of which a SNP call
        falling under is 'discarded'
  - coverage:
      type: integer
      description: |
        Minimum number of a reads that a position must be covered by to be
        reported
  - homozygous_freq:
      type: integer
      description: Fraction of reads a base must have to be called 'homozygous'
  - heterozygous_freq:
      type: integer
      description: |
        Fraction of which whereby if a call falls above this value, and lower
        than the homozygous threshold, a base will be called 'heterozygous'.
  - - meta5:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - gff_exclude:
        type: file
        description: |
          file listing positions that will be 'filtered' (i.e. ignored)
          (Optional)
        pattern: "*.vcf"
        ontologies: []
output:
  full_alignment:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - fullAlignment.fasta.gz:
          type: file
          description: Fasta a fasta file of all positions contained in the VCF
            files i.e. including ref calls
          pattern: ".fasta.gz"
          ontologies:
            - edam: <http://edamontology.org/format_3615>
            - edam: <http://edamontology.org/format_3989>
  info_txt:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - info.txt:
          type: file
          description: Information about the run
          pattern: ".txt"
          ontologies: []
  snp_alignment:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - snpAlignment.fasta.gz:
          type: file
          description: A fasta file of just SNP positions with samples only
          pattern: ".fasta.gz"
          ontologies:
            - edam: <http://edamontology.org/format_3615>
            - edam: <http://edamontology.org/format_3989>
  snp_genome_alignment:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - snpAlignmentIncludingRefGenome.fasta.gz:
          type: file
          description: A fasta file of just SNP positions with reference genome
          pattern: ".fasta.gz"
          ontologies:
            - edam: <http://edamontology.org/format_3615>
            - edam: <http://edamontology.org/format_3989>
  snpstatistics:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - snpStatistics.tsv:
          type: file
          description: Some basic statistics about the SNP calls of each sample
          pattern: ".tsv"
          ontologies:
            - edam: <http://edamontology.org/format_3475>
  snptable:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - snpTable.tsv:
          type: file
          description: Basic SNP table of combined positions taken from each VCF
            file
          pattern: ".tsv"
          ontologies:
            - edam: <http://edamontology.org/format_3475>
  snptable_snpeff:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - snpTableForSnpEff.tsv:
          type: file
          description: Input file for SnpEff
          pattern: ".tsv"
          ontologies:
            - edam: <http://edamontology.org/format_3475>
  snptable_uncertainty:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - snpTableWithUncertaintyCalls.tsv:
          type: file
          description: Same as above, but with lower case characters indicating
            uncertain calls
          pattern: ".tsv"
          ontologies:
            - edam: <http://edamontology.org/format_3475>
  structure_genotypes:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - structureGenotypes.tsv:
          type: file
          description: Input file for STRUCTURE
          pattern: ".tsv"
          ontologies:
            - edam: <http://edamontology.org/format_3475>
  structure_genotypes_nomissing:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - structureGenotypes_noMissingData-Columns.tsv:
          type: file
          description: Alternate input file for STRUCTURE
          pattern: ".tsv"
          ontologies:
            - edam: <http://edamontology.org/format_3475>
  json:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - MultiVCFAnalyzer.json:
          type: file
          description: Summary statistics in MultiQC JSON format
          pattern: ".json"
          ontologies:
            - edam: <http://edamontology.org/format_3464>
  versions_multivcfanalyzer:
    - - ${task.process}:
          type: string
          description: The name of the process
      - multivcfanalyzer:
          type: string
          description: The name of the tool
      - multivcfanalyzer -h | head -n 1 | cut -f 3 -d " ":
          type: eval
          description: The expression to obtain the version of the tool
  versions_tabix:
    - - ${task.process}:
          type: string
          description: The name of the process
      - tabix:
          type: string
          description: The name of the tool
      - tabix -h 2>&1 | grep Version | cut -f 2 -d " ":
          type: eval
          description: The expression to obtain the version of the tool
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The name of the process
      - multivcfanalyzer:
          type: string
          description: The name of the tool
      - multivcfanalyzer -h | head -n 1 | cut -f 3 -d " ":
          type: eval
          description: The expression to obtain the version of the tool
    - - ${task.process}:
          type: string
          description: The name of the process
      - tabix:
          type: string
          description: The name of the tool
      - tabix -h 2>&1 | grep Version | cut -f 2 -d " ":
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@jfy133"
maintainers:
  - "@jfy133"
  - "@TCLamnidis"

And here’s the errors:

Match meta.ymls in one of the subdirectories of modules/nf-core............................Failed
- hook id: check-jsonschema
- exit code: 1

Schema validation errors were encountered.
  modules/nf-core/multivcfanalyzer/meta.yml::$.output.versions_multivcfanalyzer[0]: [{'${task.process}': {'type': 'string', 'description': 'The name of the process'}}, {'multivcfanalyzer': {'type': 'string', 'description': 'The name of the tool'}}, {'multivcfanalyzer -h | head -n 1 | cut -f 3 -d " "': {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}}] is not valid under any of the given schemas
  Underlying errors caused this.

  Best Match:
    $.output.versions_multivcfanalyzer[0]: [{'${task.process}': {'type': 'string', 'description': 'The name of the process'}}, {'multivcfanalyzer': {'type': 'string', 'description': 'The name of the tool'}}, {'multivcfanalyzer -h | head -n 1 | cut -f 3 -d " "': {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}}] is not of type 'object'
  Best Deep Match:
    $.output.versions_multivcfanalyzer[0][2]['multivcfanalyzer -h | head -n 1 | cut -f 3 -d " "'].type: 'eval' is not one of ['map', 'file', 'directory', 'string', 'integer', 'float', 'boolean', 'list']
  modules/nf-core/multivcfanalyzer/meta.yml::$.output.versions_tabix[0]: [{'${task.process}': {'type': 'string', 'description': 'The name of the process'}}, {'tabix': {'type': 'string', 'description': 'The name of the tool'}}, {'tabix -h 2>&1 | grep Version | cut -f 2 -d " "': {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}}] is not valid under any of the given schemas
  Underlying errors caused this.

  Best Match:
    $.output.versions_tabix[0]: [{'${task.process}': {'type': 'string', 'description': 'The name of the process'}}, {'tabix': {'type': 'string', 'description': 'The name of the tool'}}, {'tabix -h 2>&1 | grep Version | cut -f 2 -d " "': {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}}] is not of type 'object'
  Best Deep Match:
    $.output.versions_tabix[0][2]['tabix -h 2>&1 | grep Version | cut -f 2 -d " "'].type: 'eval' is not one of ['map', 'file', 'directory', 'string', 'integer', 'float', 'boolean', 'list']

could it be that your branch is very outdated with respect to

master

and therefor has the old schema file

yes…. homer disappear

you are welcome!